Treeing partial sequences

Ed Rybicki ED at micro.uct.ac.za
Wed Mar 10 02:14:51 EST 1993


> From:          mkkuhner at phylo.genetics.washington.edu (Mary K. Kuhner)
> In article <1993Mar8.190355.21445 at husc3.harvard.edu> robison1 at husc10.harvard.edu (Keith Robison) writes:
>
> >I would like to make a tree for a gene family, but the problem is that
>
> >robison at biosun.harvard.edu
>
> Two possible ideas (I certainly won't claim to know the best way):
>
> 1.  Use a distance method such as neighbor-joining, and calculate
>
> 2.  Make a number of subtrees (using whatever method you would normally
>
> In either case, the resulting phylogeny should not be taken very
> seriously, as in my experience there is not enough information in a gene
> fragment to make a good phylogeny estimate.  At best it's a rough
> sketch.

I would argue with the above statement (...not enough info...): this
should perhaps read "...not NECESSARILY enough info...".  In my experience
with plant viruses, I get very much the same results, with the
geminiviruses, with 254 bp compared to what I get with 2700 bp (whole
genome) - same with potyviruses; CP gives same phylogeny as whole genome
same as 3' untranslated region.

Remember, he said A DECENT IDEA (or words to same effect) - and using
something like CLUSTALV or PileUp on a mixture of whole and partial
sequences appears to work quite well, as the relationships you get are
those between comparable areas of the sequences (personal experience:
comparing whole single picornavirus polyproteins with putative picornaviral
equivalents and 2-part proteins from two groups of plant viruses, worked
well).

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